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NM_004360.5(CDH1):c.1711G>A (p.Gly571Ser) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Feb 10, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000165027.4

Allele description [Variation Report for NM_004360.5(CDH1):c.1711G>A (p.Gly571Ser)]

NM_004360.5(CDH1):c.1711G>A (p.Gly571Ser)

Gene:
CDH1:cadherin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_004360.5(CDH1):c.1711G>A (p.Gly571Ser)
HGVS:
  • NC_000016.10:g.68819425G>A
  • NG_008021.1:g.87134G>A
  • NM_001317184.2:c.1528G>A
  • NM_001317185.2:c.163G>A
  • NM_001317186.2:c.-254-2576G>A
  • NM_004360.5:c.1711G>AMANE SELECT
  • NP_001304113.1:p.Gly510Ser
  • NP_001304114.1:p.Gly55Ser
  • NP_004351.1:p.Gly571Ser
  • LRG_301t1:c.1711G>A
  • LRG_301:g.87134G>A
  • NC_000016.9:g.68853328G>A
  • NM_004360.3:c.1711G>A
  • p.G571S
  • p.Gly571Ser
Protein change:
G510S
Links:
dbSNP: rs786202290
NCBI 1000 Genomes Browser:
rs786202290
Molecular consequence:
  • NM_001317186.2:c.-254-2576G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317184.2:c.1528G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317185.2:c.163G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.1711G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000215724Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Feb 10, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Ambry Genetics, SCV000215724.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.1711G>A variant (also known as p.G571S), located in coding exon 11 of the CDH1 gene, results from a G to A substitution at nucleotide position 1711. The amino acid change results in glycine to serine at codon 571, an amino acid with similar properties. However, this change occurs in the last base pair of coding exon 11, which makes it likely to have some effect on normal mRNA splicing. This alteration has been detected in a family with a clinical history consistent with hereditary diffuse gastric cancer (Ambry internal data). RNA analysis has shown to cause aberrant splicing in patient-derived lymphoblast cells (Casadei S et al. Proc Natl Acad Sci U S A, 2019 Dec;:). This nucleotide position is completely conserved on sequence alignment. This amino acid position is highly conserved in available vertebrate species. In silico splice site analysis for this alteration is inconclusive and direct evidence is insufficient at this time (Ambry internal data). In silico splice site analysis for this alteration is inconclusive. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 20, 2024